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- PDB-4w7z: Tetrameric BAP29 vDED without disulfide bonds -

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Basic information

Entry
Database: PDB / ID: 4w7z
TitleTetrameric BAP29 vDED without disulfide bonds
ComponentsB-cell receptor-associated protein 29
KeywordsTRANSPORT PROTEIN / Coiled coil / nanomaterial
Function / homology
Function and homology information


protein localization to endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / osteoblast differentiation / apoptotic process / endoplasmic reticulum membrane / membrane
Similarity search - Function
B-cell receptor-associated protein 29/31 / BAP29/BAP31, transmembrane domain / Bap31/Bap29 cytoplasmic coiled-coil domain / Bap31/Bap29 transmembrane region / Bap31/Bap29 cytoplasmic coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / B-cell receptor-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQuistgaard, E.M.
CitationJournal: Chem.Commun.(Camb.) / Year: 2014
Title: A disulfide polymerized protein crystal.
Authors: Quistgaard, E.M.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-cell receptor-associated protein 29
B: B-cell receptor-associated protein 29
C: B-cell receptor-associated protein 29
D: B-cell receptor-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,77021
Polymers30,1744
Non-polymers1,59617
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12970 Å2
ΔGint-244 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.900, 115.900, 167.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21D-411-

HOH

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Components

#1: Protein
B-cell receptor-associated protein 29 / Bap29


Mass: 7543.510 Da / Num. of mol.: 4 / Fragment: UNP residues 168-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAP29, BAP29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHQ4
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.65 Å3/Da / Density % sol: 73.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 4.6
Details: The crystal grew in 1.8 M ammonium sulfate, 100 mM Na acetate pH 4.6 and 5 mM TCEP using protein purified in 20 mM Tris pH 8, 150 mM NaCl and 0.5 mM TCEP and concentrated to ~14 mg/mL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→29.27 Å / Num. obs: 28934 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rsym value: 0.072 / Net I/σ(I): 19.05
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 9.7 % / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model at lower resolution build based on selenomethionine SAD phases

Resolution: 2.2→29.265 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1192 4.12 %RANDOM
Rwork0.1834 ---
obs0.1842 28929 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 84 194 2295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082110
X-RAY DIFFRACTIONf_angle_d0.9762815
X-RAY DIFFRACTIONf_dihedral_angle_d13.861862
X-RAY DIFFRACTIONf_chiral_restr0.063305
X-RAY DIFFRACTIONf_plane_restr0.003357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.28820.20311310.19413007X-RAY DIFFRACTION98
2.2882-2.39220.24551380.1773007X-RAY DIFFRACTION99
2.3922-2.51830.17671270.17423036X-RAY DIFFRACTION99
2.5183-2.6760.20141210.17583055X-RAY DIFFRACTION99
2.676-2.88240.21461430.18223039X-RAY DIFFRACTION99
2.8824-3.17220.23771440.20213063X-RAY DIFFRACTION99
3.1722-3.63050.18961220.15473106X-RAY DIFFRACTION99
3.6305-4.57120.14321300.16063144X-RAY DIFFRACTION100
4.5712-29.26770.22951360.21973280X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.3891-2.7283-0.53233.43280.06092.55390.1842-0.0081-0.6235-0.3575-0.22480.29540.2012-0.03050.05480.16040.00360.01690.2150.00020.1479-28.5317-32.9523-13.8982
26.2075-3.252-1.03264.1431-0.11332.40340.0536-0.20090.58740.0634-0.1026-0.4287-0.3680.18430.00170.19970.0208-0.06520.1931-0.00230.1833-27.1939-22.1152-11.3313
35.2334-1.3841-0.89082.99990.10542.46580.0931-0.3712-0.71650.0059-0.11510.19390.1761-0.111-0.07320.2174-0.02050.01910.19150.02920.1448-29.6266-33.4343-7.8907
47.3664-2.4544-1.45923.11690.11033.05860.0347-0.51230.58050.096-0.037-0.1923-0.20930.1307-0.03540.2699-0.0027-0.06160.2314-0.02320.1299-26.6039-24.6251-5.7458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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